Contacts of the helix formed by residues 420 - 453 (chain P) in PDB entry 5GJQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 420 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418P PRO* 3.9 11.8 - - - +
419P LYS* 1.3 87.5 - - - +
421P PRO* 1.3 68.6 - - + -
422P ASN* 2.1 23.9 + - + +
423P ASN* 2.2 29.2 + - - +
424P LEU* 4.2 4.9 - - - -
392Q PRO* 6.2 3.4 - - - -
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Residues in contact with PRO 421 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420P ASP* 1.3 99.2 - - + +
422P ASN* 1.3 63.8 + - + +
423P ASN 3.3 0.2 - - - -
424P LEU* 3.4 14.4 + - + +
425P LEU* 2.9 32.5 + - - +
247U LYS 4.8 0.4 - - - -
248U ALA* 3.3 41.5 - - + +
251U LEU* 4.1 31.0 - - + -
252U LYS* 5.0 9.4 - - + +
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Residues in contact with ASN 422 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420P ASP* 2.1 14.8 + - + +
421P PRO* 1.3 78.3 - - + +
423P ASN* 1.3 60.4 + - - +
425P LEU* 3.3 5.5 + - - +
426P ASN* 3.1 28.1 + - - +
252U LYS* 3.2 27.6 - - - +
234V TYR* 3.3 23.4 - - - +
235V SER* 3.5 19.3 + - - +
238V CYS* 3.0 30.4 - - - -
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Residues in contact with ASN 423 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418P PRO 4.7 1.0 + - - -
419P LYS* 3.1 40.4 - - + +
420P ASP* 2.2 27.8 + - - +
422P ASN* 1.3 68.9 - - - +
424P LEU* 1.3 64.9 + - - +
426P ASN* 3.2 21.6 + - - +
427P ASP* 3.3 20.4 + - - +
235V SER* 5.8 1.9 - - - -
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Residues in contact with LEU 424 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419P LYS* 4.6 11.4 - - + +
420P ASP 3.5 4.2 + - - +
421P PRO* 3.4 27.1 + - + +
423P ASN* 1.3 78.4 - - - +
425P LEU* 1.3 62.4 + - - +
427P ASP* 3.4 16.5 + - - +
428P TRP* 3.2 17.8 + - - +
431P LYS* 5.2 1.4 + - - -
244U GLU* 4.0 41.1 - - + +
245U PHE* 4.8 1.3 - - - +
248U ALA* 4.1 8.1 - - + +
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Residues in contact with LEU 425 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421P PRO 2.9 14.9 + - - +
422P ASN* 3.6 5.6 - - - +
423P ASN 3.1 0.2 - - - -
424P LEU* 1.3 76.8 - - - +
426P ASN* 1.3 54.0 + - - +
428P TRP* 3.0 42.2 + - + +
429P SER* 2.7 37.4 + - - -
245U PHE* 4.0 11.2 - - + -
248U ALA* 3.8 17.5 - - + +
249U PHE* 3.7 30.5 - - + +
252U LYS* 4.0 3.6 - - + -
231V LEU* 5.3 0.9 - - + -
234V TYR* 3.4 44.4 - - + +
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Residues in contact with ASN 426 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422P ASN 3.1 16.3 + - - +
423P ASN* 3.2 18.4 + - - +
425P LEU* 1.3 77.5 - - - +
427P ASP* 1.3 54.2 + - - +
429P SER* 2.9 12.8 + - - +
430P GLN* 2.7 41.6 + - + +
233V ASP* 2.5 33.8 + - - +
234V TYR* 3.6 11.8 + - - +
235V SER* 3.4 16.1 + - - -
----------------------------------------------------------
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Residues in contact with ASP 427 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423P ASN* 3.4 16.6 - - - +
424P LEU* 3.5 17.7 - - - +
425P LEU 3.2 0.2 - - - -
426P ASN* 1.3 78.7 - - - +
428P TRP* 1.3 56.9 + - - +
430P GLN* 3.7 11.9 - - - +
431P LYS* 2.8 51.5 + - - +
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Residues in contact with TRP 428 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424P LEU 3.2 8.5 + - - +
425P LEU* 3.0 40.4 + - + +
427P ASP* 1.3 77.3 - - - +
429P SER* 1.3 71.0 + - - +
431P LYS* 3.2 17.7 + - + +
432P LEU* 3.0 45.1 + - + +
238U PRO* 3.3 41.0 - - + +
245U PHE* 3.1 35.9 - + + -
249U PHE* 5.5 2.2 - + - -
231V LEU* 3.8 21.8 - - + -
302V ALA* 4.7 8.7 - - + -
305V ASP* 3.0 50.0 - - + -
306V THR* 4.6 2.5 - - - -
309V PHE* 5.2 0.7 - - + -
310V LYS* 5.6 2.6 - - - +
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Residues in contact with SER 429 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425P LEU* 2.7 17.4 + - - -
426P ASN* 2.9 21.4 + - - -
428P TRP* 1.3 75.4 - - - +
430P GLN* 1.3 66.7 + - - +
432P LEU* 3.4 14.6 + - - +
433P ASN* 3.3 29.7 + - - +
231V LEU* 4.0 30.7 + - - -
232V GLN 5.5 0.7 - - - -
233V ASP* 5.4 2.7 - - - -
234V TYR* 6.0 2.7 - - - -
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Residues in contact with GLN 430 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426P ASN* 2.7 25.4 + - + +
427P ASP* 3.7 12.4 - - - +
429P SER* 1.3 73.2 + - - +
431P LYS* 1.3 65.7 + - - +
433P ASN* 3.4 14.1 + - - +
434P SER* 3.1 25.5 + - - -
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Residues in contact with LYS 431 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424P LEU 5.2 1.4 + - - -
427P ASP* 2.8 43.2 + - - +
428P TRP* 3.2 23.1 + - + +
430P GLN* 1.3 73.8 - - - +
432P LEU* 1.3 66.6 + - + +
434P SER* 3.3 6.4 + - - -
435P LEU* 3.0 24.2 + - - +
236U LEU* 3.9 32.8 - - + +
238U PRO* 5.3 7.4 - - + +
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Residues in contact with LEU 432 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428P TRP* 3.0 62.6 + - + +
429P SER* 3.5 12.8 - - - +
431P LYS* 1.3 76.9 - - + +
433P ASN* 1.3 63.1 + - - +
435P LEU* 3.3 10.3 + - + +
436P MET* 3.2 25.6 + - + +
238U PRO* 4.2 6.7 - - + -
229V LEU* 4.5 9.2 - - + +
230V THR* 6.4 0.4 - - - -
231V LEU* 5.2 4.7 - - + +
305V ASP* 3.7 17.5 - - - +
309V PHE* 3.1 41.2 - - + -
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Residues in contact with ASN 433 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429P SER* 3.3 18.4 + - - +
430P GLN* 3.5 17.5 - - + +
432P LEU* 1.3 81.8 - - - +
434P SER* 1.3 62.5 + - - +
436P MET* 3.1 21.1 + - - +
437P SER* 3.4 6.9 + - - -
226V MET* 5.6 2.1 - - - +
230V THR* 4.6 19.2 - - - +
231V LEU 5.4 3.5 + - - -
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Residues in contact with SER 434 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430P GLN 3.1 14.5 + - - -
431P LYS* 3.7 6.5 - - - -
433P ASN* 1.3 80.1 - - - +
435P LEU* 1.3 60.2 + - - +
437P SER* 2.4 27.5 + - - -
438P LEU* 3.3 11.3 + - - +
236U LEU* 3.8 15.0 - - - -
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Residues in contact with LEU 435 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356O TRP* 4.1 11.9 - - + -
431P LYS 3.0 13.7 + - - +
432P LEU* 3.4 11.0 - - + +
434P SER* 1.3 75.0 - - - +
436P MET* 1.3 72.8 + - + +
438P LEU* 2.9 8.9 + - - +
439P VAL* 2.7 57.2 + - + -
233U VAL* 4.0 28.5 - - + +
236U LEU* 3.4 27.1 - - + +
237U LEU* 4.2 18.6 - - + -
238U PRO* 5.0 2.7 - - + -
309V PHE* 4.8 11.9 - - + -
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Residues in contact with MET 436 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356O TRP* 5.4 0.2 - - + -
432P LEU* 3.2 11.6 + - + +
433P ASN* 3.1 15.0 + - - +
435P LEU* 1.3 89.8 - - + +
437P SER* 1.3 51.0 + - - +
439P VAL* 3.1 16.2 + - - +
440P ASN* 2.5 39.8 + - + +
201U LEU* 3.7 24.2 - - + -
225V TRP* 3.7 20.8 - - + -
226V MET* 3.4 36.3 - - + +
229V LEU* 4.9 11.2 - - + -
309V PHE* 3.9 24.9 - - + -
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Residues in contact with SER 437 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433P ASN 3.4 4.0 + - - -
434P SER* 2.4 34.5 + - - -
436P MET* 1.3 78.4 - - - +
438P LEU* 1.3 56.9 + - - +
440P ASN* 4.2 7.0 - - - +
441P LYS* 2.5 41.3 + - - +
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Residues in contact with LEU 438 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434P SER 3.6 7.9 - - - +
435P LEU* 2.9 9.0 + - - +
437P SER* 1.3 80.2 + - - +
439P VAL* 1.3 49.6 + - - +
441P LYS* 4.7 2.2 - - + -
442P THR* 2.6 42.7 + - - +
229U GLN* 4.6 21.2 - - + +
232U ASP* 3.5 50.9 - - + +
233U VAL* 4.0 14.8 - - + +
236U LEU* 3.6 23.3 - - + -
----------------------------------------------------------
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Residues in contact with VAL 439 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356O TRP* 4.6 11.2 - - + -
435P LEU* 2.7 42.8 + - + +
436P MET* 3.5 19.5 - - - +
438P LEU* 1.3 75.2 - - - +
440P ASN* 1.3 55.7 + - - +
442P THR* 3.2 13.0 - - + +
443P THR* 3.1 21.3 - - - +
201U LEU* 5.3 2.7 - - + -
204U LYS* 4.2 21.3 - - + -
205U LEU* 5.0 11.9 - - + -
208U ILE* 4.8 6.2 - - + +
233U VAL* 4.3 13.9 - - + -
225V TRP* 4.7 8.1 - - + -
----------------------------------------------------------
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Residues in contact with ASN 440 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436P MET* 2.5 30.6 + - + +
437P SER* 4.0 6.6 - - - +
439P VAL* 1.3 66.6 - - - +
441P LYS* 1.3 64.1 + - - +
442P THR 3.1 1.1 - - - -
443P THR* 2.2 40.0 + - - +
157U HIS* 3.3 22.1 + - - -
159U THR* 6.1 1.6 - - - -
204U LYS* 5.3 6.8 - - - +
225V TRP* 6.1 6.5 - - + -
226V MET* 6.4 0.9 - - + -
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Residues in contact with LYS 441 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437P SER* 2.5 26.1 + - - +
438P LEU* 4.6 2.5 - - + +
440P ASN* 1.3 73.8 - - - +
442P THR* 1.3 62.4 + - - +
443P THR 3.2 0.7 + - - -
444P HIS* 3.7 10.6 + - - +
445P LEU* 4.0 18.0 + - + +
156U GLU* 5.2 7.0 - - - -
157U HIS* 3.3 33.4 + - + -
229U GLN* 4.0 22.4 - - - +
----------------------------------------------------------
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Residues in contact with THR 442 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438P LEU 2.6 28.5 + - - +
439P VAL* 3.2 18.8 - - - +
440P ASN 3.1 0.2 - - - -
441P LYS* 1.3 79.6 - - - +
443P THR* 1.3 59.8 + - - +
445P LEU* 3.6 5.8 + - - +
446P ILE* 3.5 19.8 + - - +
208U ILE* 3.5 28.8 - - + +
226U ILE* 4.2 16.1 - - - +
229U GLN* 3.4 31.6 + - - +
230U LEU* 4.5 6.7 - - + +
233U VAL* 5.6 2.0 - - + -
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Residues in contact with THR 443 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439P VAL 3.1 19.5 - - - +
440P ASN* 2.2 36.2 + - - -
442P THR* 1.3 78.0 - - + +
444P HIS* 1.4 57.8 + - - -
446P ILE* 3.1 30.0 + - - +
447P ALA* 3.2 8.6 + - - +
157U HIS* 4.2 2.9 - - - -
204U LYS* 3.3 40.1 + - + +
207U ASP* 5.4 4.0 - - + +
208U ILE* 5.5 5.4 - - + -
----------------------------------------------------------
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Residues in contact with HIS 444 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441P LYS 3.7 5.0 + - - +
443P THR* 1.4 73.8 + - - +
445P LEU* 1.3 58.2 + - + +
447P ALA* 3.7 8.8 - - + +
448P LYS* 2.6 49.8 + - + +
101U LEU* 3.9 17.0 - - + -
138U TYR* 2.6 54.6 + + - -
155U PHE* 2.6 33.9 + - - +
156U GLU* 4.1 0.7 - - - -
157U HIS* 3.1 40.4 - - + +
----------------------------------------------------------
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Residues in contact with LEU 445 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441P LYS* 4.0 19.0 + - + +
442P THR 3.6 6.8 + - - +
443P THR 3.4 0.8 - - - -
444P HIS* 1.3 80.0 - - + +
446P ILE* 1.3 57.6 + - - +
448P LYS* 3.1 22.0 + - + +
449P GLU* 2.7 39.3 + - + +
223U ASN* 6.3 0.2 - - + -
225U GLN* 4.5 23.8 - - + +
226U ILE* 3.8 30.3 - - + +
229U GLN* 4.9 12.6 - - - +
----------------------------------------------------------
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Residues in contact with ILE 446 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442P THR* 3.5 17.3 - - - +
443P THR* 3.1 11.2 + - - +
445P LEU* 1.3 75.4 - - - +
447P ALA* 1.3 59.7 + - + +
449P GLU* 3.0 17.0 - - - +
450P GLU* 2.8 41.3 + - - +
207U ASP* 4.5 15.0 - - + +
208U ILE* 4.5 23.6 - - + -
211U TYR* 3.2 52.3 - - + -
226U ILE* 4.3 14.6 - - + -
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Residues in contact with ALA 447 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443P THR 3.2 9.2 + - - +
444P HIS* 3.7 15.9 - - + +
445P LEU 3.2 0.6 - - - -
446P ILE* 1.3 75.5 - - + +
448P LYS* 1.3 67.7 + - - +
449P GLU 3.1 2.0 - - - -
450P GLU* 3.0 15.1 + - - +
451P MET* 2.9 35.0 + - + +
100U LYS* 5.0 17.5 - - + -
101U LEU* 5.1 3.6 - - + -
138U TYR* 5.5 2.9 - - - +
----------------------------------------------------------
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Residues in contact with LYS 448 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444P HIS* 2.6 44.9 + - + +
445P LEU* 3.5 22.7 - - + +
447P ALA* 1.3 72.7 - - - +
449P GLU* 1.3 56.0 + - + +
451P MET* 3.6 1.2 + - - +
452P ILE* 2.7 56.4 + - + +
101U LEU* 4.3 15.5 - - + +
154U THR* 1.9 50.2 + - - +
155U PHE* 3.8 14.4 - - + +
----------------------------------------------------------
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Residues in contact with GLU 449 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445P LEU* 2.7 22.6 + - + +
446P ILE* 3.0 19.8 - - - +
448P LYS* 1.3 76.5 - - + +
450P GLU* 1.3 53.1 + - + +
452P ILE* 4.4 4.7 - - - +
453P HIS* 2.3 60.2 + - + +
211U TYR* 2.9 27.1 + - + -
223U ASN* 2.3 38.2 + - - +
226U ILE* 2.5 22.2 - - + +
----------------------------------------------------------
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Residues in contact with GLU 450 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446P ILE* 2.8 39.3 - - + +
447P ALA* 3.0 16.0 + - - +
449P GLU* 1.3 77.8 - - + +
451P MET* 1.3 76.0 + - + +
453P HIS* 4.6 0.4 - - - -
454P ASN* 3.1 34.9 + - - +
100U LYS* 5.3 5.5 - - - -
211U TYR* 5.1 9.1 - - + +
214U LYS* 4.2 21.8 + - + +
----------------------------------------------------------
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Residues in contact with MET 451 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447P ALA* 2.9 23.0 + - - +
448P LYS 3.9 3.8 - - - +
450P GLU* 1.3 98.6 - - + +
452P ILE* 1.3 61.3 + - + +
453P HIS 3.7 0.2 + - - -
454P ASN* 3.9 9.0 + - - -
100U LYS* 3.7 35.0 - - + -
101U LEU* 4.2 36.1 - - + +
102U HIS* 4.6 19.4 - - - +
103U LYS* 5.9 1.6 - - - +
----------------------------------------------------------
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Residues in contact with ILE 452 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448P LYS* 2.7 55.0 + - + +
449P GLU* 4.0 4.3 - - - +
451P MET* 1.3 78.0 - - + +
453P HIS* 1.3 72.1 + - + +
454P ASN* 4.3 1.4 + - - -
101U LEU* 6.0 1.8 - - + -
102U HIS 5.5 4.7 - - - +
106U ILE* 5.5 12.6 - - + -
154U THR* 5.1 0.9 - - - +
----------------------------------------------------------
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Residues in contact with HIS 453 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449P GLU* 2.3 47.5 + - + +
450P GLU* 4.6 0.7 - - - -
452P ILE* 1.3 82.0 - - + +
454P ASN* 1.3 86.7 + - - +
219U LYS* 4.9 8.4 + - - +
221U PRO* 3.9 29.7 - - + +
223U ASN* 5.1 9.9 + - - -
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il